The use of capture probes attached to a substrate within an electrochemical biosensing device, such as a nanostructured microelectrode (NME), for biomarker analysis is known in the art. As the probe captures its negatively charged target it causes increased negative charge near the surface of the electrode which can be detected electrochemically by an increase in current as a potential is applied. The NME is typically electrochemically plated onto patterned gold electrodes on a glass or semi-conducting substrate, such as silicon. Silicon or glass wafer lithographic methods which often involve silicon dioxide (SiO2) or silicon nitride (Si3N4), layer deposition and patterning are well developed for the electronics industry but these substrates are not typically designed for exposure to solutions, a common practice in electrochemical sensing applications. Dioxide layers tend to be more porous, which may cause biomolecule adsorption or trapping, which in turn poses problems with the detection of targets. Further, penetration of the electrolyte solution to underlying layers of the substrate may have undesirable effects during electrochemical sensing. The isoelectric points of silicon dioxide (pH1.7-3.5) and silicon nitride (pH9) are significantly different from each other and from the solutions used during electrochemical sensing. Additionally, the fabrication, dicing, and etching processes used to create silicon or glass chips suitable for NME growth sometimes leave surface contaminants or residues that affect the water contact angle. This effect results in variable surface wetting that has downstream effects in sensor fabrication, probe deposition, the assay, and microfluidic cassette functionality. There is therefore a need for silicon or glass substrates with chemical surface modification that can be utilized in procedures involving wet chemistry and biosensing that addresses the aforementioned problems. There is also a need for a consistent hydrophobic surface, which prevents wicking effects and spreading of solutions which can occur when depositing multiple probe-containing droplets on a single chip to functionalize individual NMEs with unique probes.